Furthermore, we utilize the RSS difference to infer the positioning confidence.
Supplementary Table 1 List of the traits included in the drought QTL database (DOC 46 kb) Supplementary Table 2 List of QTLs and meta-QTLs (in bold) for 10 root traits, plant height (chromosome 1 only) and duration (chromosomes 3 and 6 only) with their position, confidence interval and probability of belonging to a cluster (M1 to M8).
Information on the precise positions or confidence intervals of the putative QTLs, for example, was often absent from the papers, with just indication of the flanking markers.
The positions and confidence intervals of ovine and bovine QTL and blocks of conserved synteny across both species were identified and aligned to the genomes of both species.
For a given model, a Gaussian mixture approach was applied to jointly perform a quantitative clustering of the projected QTLs and estimate meta-QTL positions and confidence intervals by maximizing the likelihood of the initial QTL positions.
This command enabled the homothetic projection of the individual QTL positions and confidence intervals based on a scaling rule between QTL-flanking marker positions on the individual maps and on the consensus map.
Finally, the QTL meta-analysis algorithm, computed in the QTLClust command of the software, was used to determine the most likely number of meta-QTL on a given chromosome and to estimate their corresponding positions and confidence intervals.
On a given chromosome, projected independent QTL were clustered into all possible numbers of hypothetic clusters of meta-QTL (K), for which a Gaussian mixture model estimates meta-QTL positions and confidence intervals [ 17].
As a result, each meta-QTL position and confidence interval correspond to the consensus position of all the individual QTLs attributed to this meta-QTL, weighted by their individual accuracies and probability of being attributed to the meta-QTL.
The remaining three genes were not positioned with confidence on the RH map so the positions predicted by the virtual sheep genome could not be confirmed.
